Palm Beach County has a cooperative program involving forty (40) co-permittees, the Florida Department of Environment Protection (FDEP), and the United States Environmental Protection Agency (EPA) to administer annual stormwater NPDES permitting.  Northern Palm Beach County Improvement District (NPBCID) acts as the lead permittee for the Palm Beach County group, and the City of Boynton Beach participates as one of the co-permittees.   A Steering Committee was formed in 1991 to coordinate and facilitate joint activities within the Palm Beach County MS4 NPDES program. A consulting engineering firm, Mock Roos, Inc., acts as staff to the Steering Committee, assisting with the administration of the program.

The Municipal Separate Storm Sewer System (MS4) National Pollutant Discharge Elimination System (NPDES) is a federal program designed to reduce stormwater pollutant discharges to receiving waters of the United States.  In 1987, the EPA was required under the Clean Water Act to establish final regulations governing stormwater discharge permit application requirements. In 1990, the Federal Register indicated that the Palm Beach County area was to begin compliance with the program. In 1997, the first 5-year permit was issued to Palm Beach County's forty (40) co-permittees. The second term permit was issued in November 2002, and the third term permit was effective March 2011.  The fourth cycle permit was issued by FDEP on September 8, 2016.